I have the RY set and found them perfectly balanced in volume and tone without having to fiddle much with pickup height.
But even if the pickup heights were extremely mismatched you still should not get a vast difference in output. The RY bridge is wound a lot hotter than the RY neck to match each other in volume. Check the DC resistance with a digital multimeter (DMM). You should get about 7k to 8k ohms for the neck and about 14k to 15k for the bridge pickup.
If the readings are in that range listen for noise. Does the bridge pickup hum noticeably more than the neck pickup? If so, check the bridge pickup's wiring (do you have a 4 conductor)? The BKP main site has the standard wiring diagram.
If everything is wired correctly, the problem could be in the associated wiring circuitry. Try swapping the connections of the pickups, i.e. solder the neck pickup to where the bridge pickup was soldered and vice versa. If the bridge pickup is still lower in volume, then it's not the circuitry.
Please let us know how you get on.
Good luck
Stephan